Fred Hutchinson Cancer Research Center

About: Fred Hutchinson Cancer Research Center is a nonprofit organization based out in Cape Town, South Africa. It is known for research contribution in the topics: Population & Transplantation. The organization has 12322 authors who have published 30954 publications receiving 2288772 citations. The organization is also known as: Fred Hutch & The Hutch.

Identification of High-Copy Disruptors of Telomeric Silencing in Saccharomyces cerevisiae

Abstract: The ends of chromosomes in Saccharomyces cerevisiae initiate a repressive chromatin structure that spreads internally and inhibits the transcription of nearby genes, a phenomenon termed telomeric silencing. To investigate the molecular basis of this process, we carried out a genetic screen to identify genes whose overexpression disrupts telomeric silencing. We thus isolated 10 DOT genes (disruptor of telomeric silencing). Among these were genes encoding chromatin component Sir4p, DNA helicase Dna2p, ribosomal protein L32, and two proteins of unknown function, Asf1p and Ifh1p. The collection also included genes that had not previously been identified: DOT1, DOT4, DOT5, DOT6, and TLC1, which encodes the RNA template component of telomerase. With the exception of TLC1, all these genes, particularly DOT1 and DOT4, also reduced silencing at other repressed loci (HM loci and rDNA) when overexpressed. Moreover, deletion of the latter two genes weakened silencing as well, suggesting that DOT1 and DOT4 normally play important roles in gene repression. DOT1 deletion also affected telomere tract length. The function of Dot1p is not known. The sequence of Dot4p suggests that it is a ubiquitin-processing protease. Taken together, the DOT genes include both components and regulators of silent chromatin.

Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells.

Abstract: Transcriptional silencing in mammals is often associated with promoter methylation. However, a considerable number of genomic methylated CpGs exist in transposable elements, which are frequently found in intronic regions. To determine whether intragenic methylation influences transcription efficiency, we used the Cre/loxP-based system, RMCE, to introduce a transgene, methylated exclusively in a region downstream of the promoter, into a specific genomic site. This methylation pattern was maintained in vivo, and yielded a clear decrease in transgene expression relative to an unmethylated control. Notably, RNA polymerase II (Pol II) was depleted exclusively in the methylated region, as was histone H3 di- and trimethylated on Lys4 and acetylated on Lys9 and Lys14. As the methylated region adopts a closed chromatin structure in vivo, we propose that dense intragenic DNA methylation in mammalian cells initiates formation of a chromatin structure that reduces the efficiency of Pol II elongation.

Trends in Dietary Supplement Use Among US Adults From 1999-2012.

Abstract: Importance Dietary supplements are commonly used by US adults; yet, little is known about recent trends in supplement use. Objective To report trends in dietary supplement use among US adults. Design, Setting, and Participants Serial cross-sectional study using nationally representative data from the National Health and Nutrition Examination Survey (NHANES) collected between 1999 and 2012. Participants include noninstitutionalized adults residing in the United States, surveyed over 7 continuous 2-year cycles (sample size per cycle, 4863 to 6213). Exposures Calendar time, as represented by NHANES cycle. Main Outcomes and Measures In an in-home interview, participants were queried on use of supplements in the preceding 30 days to estimate the prevalence of use within each NHANES cycle, and trends were evaluated across cycles. Outcomes included use of any supplements; use of multivitamins/multiminerals (MVMM; defined as a product containing ≥10 vitamins and/or minerals); and use of individual vitamins, minerals, and nonvitamin, nonmineral supplements. Data were analyzed overall and by population subgroup (including age, sex, race/ethnicity, and educational status), and were weighted to be nationally representative. Results A total of 37 958 adults were included in the study (weighted mean age, 46.4 years; women, 52.0% ), with an overall response rate of 74%. Overall, the use of supplements remained stable between 1999 and 2012, with 52% of US adults reporting use of any supplements in 2011-2012 ( P for trend = .19). This trend varied by population subgroup. Use of MVMM decreased, with 37% reporting use of MVMM in 1999-2000 and 31% reporting use in 2011-2012 (difference, −5.7% [95% CI, −8.6% to −2.7%], P for trend P for trend P for trend Conclusions and Relevance Among adults in the United States, overall use of dietary supplements remained stable from 1999-2012, use of MVMM decreased, and trends in use of individual supplements varied and were heterogeneous by population subgroups.

Neutralizing Antibodies Correlate with Protection from SARS-CoV-2 in Humans during a Fishery Vessel Outbreak with a High Attack Rate.

Abstract: The development of vaccines against SARS-CoV-2 would be greatly facilitated by the identification of immunological correlates of protection in humans. However, to date, studies on protective immunity have been performed only in animal models and correlates of protection have not been established in humans. Here, we describe an outbreak of SARS-CoV-2 on a fishing vessel associated with a high attack rate. Predeparture serological and viral reverse transcription-PCR (RT-PCR) testing along with repeat testing after return to shore was available for 120 of the 122 persons on board over a median follow-up of 32.5 days (range, 18.8 to 50.5 days). A total of 104 individuals had an RT-PCR-positive viral test with a cycle threshold (CT ) of <35 or seroconverted during the follow-up period, yielding an attack rate on board of 85.2% (104/122 individuals). Metagenomic sequencing of 39 viral genomes suggested that the outbreak originated largely from a single viral clade. Only three crew members tested seropositive prior to the boat's departure in initial serological screening and also had neutralizing and spike-reactive antibodies in follow-up assays. None of the crew members with neutralizing antibody titers showed evidence of bona fide viral infection or experienced any symptoms during the viral outbreak. Therefore, the presence of neutralizing antibodies from prior infection was significantly associated with protection against reinfection (Fisher's exact test, P = 0.002).

Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA

Abstract: We show that intracellular transcription of G-rich regions produces novel DNA structures, visible by electron microscopy as large (150–500 bp) loops. These G-loops are formed cotranscriptionally, and they contain G4 DNA on one strand and a stable RNA/DNA hybrid on the other. G-loop formation requires a G-rich nontemplate strand and reflects the unusual stability of the rG/dC base pair. G-loops and G4 DNA form efficiently within plasmid genomes transcribed in vitro or in Escherichia coli. These results establish that G4 DNA can form in vivo, a finding with implications for stability and maintenance of all G-rich genomic regions.